5H4S

Crystal structure of a rhamnose-binding lectin SUL-I from the toxopneustid sea urchin Toxopneustes pileolus

Summary for 5H4S

• Entry DOI: 10.2210/pdb5h4s/pdb
• Descriptor: L-rhamnose-binding lectin, alpha-L-rhamnopyranose, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: rhamnose-binding lectin, sul-i, sea urchin, toxopneustes pileolus, lectin, sugar binding protein
• Biological source: Toxopneustes pileolus (Flower urchin)
• Total number of polymer chains: 1
• Total formula weight: 31105.41

Authors

Unno, H.,Hatakeyama, T. (deposition date: 2016-11-02, release date: 2017-05-17, Last modification date: 2024-10-30)

Primary citation

Hatakeyama, T.,Ichise, A.,Unno, H.,Goda, S.,Oda, T.,Tateno, H.,Hirabayashi, J.,Sakai, H.,Nakagawa, H.
Carbohydrate recognition by the rhamnose-binding lectin SUL-I with a novel three-domain structure isolated from the venom of globiferous pedicellariae of the flower sea urchin Toxopneustes pileolus
Protein Sci., 26:1574-1583, 2017

PubMed Abstract: The globiferous pedicellariae of the venomous sea urchin Toxopneustes pileolus contains several biologically active proteins. We have cloned the cDNA of one of the toxin components, SUL-I, which is a rhamnose-binding lectin (RBL) that acts as a mitogen through binding to carbohydrate chains on target cells. Recombinant SUL-I (rSUL-I) was produced in Escherichia coli cells, and its carbohydrate-binding specificity was examined with the glycoconjugate microarray analysis, which suggested that potential target carbohydrate structures are galactose-terminated N-glycans. rSUL-I exhibited mitogenic activity for murine splenocyte cells and toxicity against Vero cells. The three-dimensional structure of the rSUL-I/l-rhamnose complex was determined by X-ray crystallographic analysis at a 1.8 Å resolution. The overall structure of rSUL-I is composed of three distinctive domains with a folding structure similar to those of CSL3, a RBL from chum salmon (Oncorhynchus keta) eggs. The bound l-rhamnose molecules are mainly recognized by rSUL-I through hydrogen bonds between its 2-, 3-, and 4-hydroxy groups and Asp, Asn, and Glu residues in the binding sites, while Tyr and Ser residues participate in the recognition mechanism. It was also inferred that SUL-I may form a dimer in solution based on the molecular size estimated via dynamic light scattering as well as possible contact regions in its crystal structure.

PubMed: 28470711
DOI: 10.1002/pro.3185

Experimental method

X-RAY DIFFRACTION (1.8 Å)